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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #377555

Research Project: Conservation and Utilization of Priority Vegetable Crop Genetic Resources and Associated Information

Location: Plant Genetic Resources Unit (PGRU)

Title: BioProject number PRJNA650148. Genotyping by sequencing of Allium cepa. BioSamples SAMN15693843-SAMN15694226

item Labate, Joanne
item GLAUBITZ, JEFFREY - Cornell University - New York
item HAVEY, MICHAEL - US Department Of Agriculture (USDA)

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 8/3/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary: Onion is an ancient crop that is highly valued in cuisines for its intense flavors. This vegetable is widely consumed in both fresh and processed forms. Onions are low in calories, high in fiber, and contain many health-beneficial properties for the heart, the immune system, protection from cancer and inflammation, and regulating blood sugar. We DNA sequenced a collection of 140 onion stocks that originated from across the globe. Patterns of genetic diversity were discovered to be related to geographic origins. Samples from the Indian subcontinent, Iran and central Asia were distinct from onions that moved westward through the Mediterranean region to Europe, and subsequent introductions to the western hemisphere, eastern Asia, Australia, and New Zealand. The results of this study will help breeders to use new sources of genetic variation to support the improvement of onion varieties throughout the world.

Technical Abstract: This BioProject consists of 49 Gbases of raw genotyping-by-sequencing (GBS) data collected in 96-plex format on an Illumina HiSeq 2000 sequencing system. Single nucleotide polymorphisms (SNPs) in onion were identified using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 Allium cepa accessions in the USDA National Plant Germplasm System (NPGS). A total of 895 high quality SNPs wee identified, of which 284 were placed onto an existing map of the F2 family. These markers are now available for other applications such as mapping morphological differences between species, marker assisted breeding, germplasm characterization, taxonomy, and DNA fingerprinting.